Found the issue. It's a rare case, specific to this map. If you load a save before Rhaskos get converted, the Team origin of the core get lost, and thus, its conversion doesn't convert the whole faction.

I moved the origin faction data to a safe location. So it shouldn't happen anymore.

As for your save the data is already lost, I can't fix it. But it's a 2min in game progress so you should be able to restart easily ;)